The additional point of damage is because a creature with only a single natural attack gets to add strength bonus times 1.5 instead of just strength bonus. With 3*1.5 being 4.5, and Pathfinder always rounding down, that becomes +4.

The HP is +2 because it has 2 HD. The CON modifier is added to each HD, just like it's added to each class level for a PC.

The Hyena perception discrepancy is a typo. 8 is the correct number (1 rank, +1 WIS, +3 class skill, +3 skill focus). The reason the perception is listed twice is because it's always listed as part of the "Senses" line, and all skills are listed as part of the "Skills" line.